R crashes when establishing a database connection via RPostgreSQL

Question

I am using R version noted below:

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
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Platform: x86_64-apple-darwin15.6.0 (64-bit)

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I am using macOS Sierra Version 10.12.6 (16G1314). Using a 3.1 GHz Intel Core i7 processor, memory 16 GB 1867 MHz DDR3, graphics card is an Intel Iris Graphics 6100 1536 MB.

Here is my R code that crashes. I've taken the host names, ports, database name, username, and password out for security reasons. The con assignment is what crashes. I am trying to connect to Redshift cluster using a code example within my organization.

library(RPostgreSQL)
drv <- dbDriver("PostgreSQL")
con <- dbConnect(
    drv,
    host = "<host name>",
    port = "<four digit port>"
    dbname = "'dbname = <database name> ssl=require'",
    user = "<user name>",
    password = "<password>"
)

Here is my R session info up until the con assignment

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] RPostgreSQL_0.6-2 DBI_0.8          

loaded via a namespace (and not attached):
[1] compiler_3.4.3

Here is the crash report with stuff removed for security reasons:

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call(RS_PostgreSQL_newConnection, drvId, con.params)
 2: postgresqlNewConnection(drv, ...)
 3: dbConnect(drv, host = "<hostname>", port = "<port>",     dbname = "'dbname = <database name> ssl=require'", user = "<user name>",     password = "<password>")
 4: dbConnect(drv, host = "<hostname>", port = "<port>",     dbname = "'dbname = <database name> ssl=require'", user = "<user name>",     password = "<password>")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

I've tried it with two Redshift clusters and ran into the same issue.

Question: How can I resolve this issue so I connect to my Redshift cluster via R?

Bonus question: Is it just me or have R releases been buggy lately?

Make that an answer. Then I’ll test it out and if it works check your answer — Brash Equilibrium, Apr 13 '18 at 16:48

score 1 · Answer 1 · answered Apr 13 '18 at 17:01

I quickly searched for and skimmed the Amazon docs for Redshift. They suggest you use a JDBC or ODBC driver. The RPostgreSQL package uses the libpq driver, so I wouldn't expect it to work with Redshift.

I suggest you use RODBC, RJDBC, or odbc, depending on which best suits your setup.

R crashes when establishing a database connection via RPostgreSQL

1 Answers1